+Open data
-Basic information
Entry | Database: PDB / ID: 4g0o | ||||||
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Title | Crystal structure of Arabidopsis thaliana AGO5 MID domain | ||||||
Components | Protein argonaute 5 | ||||||
Keywords | GENE REGULATION / MID domain / small RNA 5' nucleotide recognition | ||||||
Function / homology | Function and homology information defense response to other organism => GO:0098542 / RNAi-mediated antiviral immune response => GO:0009616 / regulatory ncRNA-mediated gene silencing / response to virus / regulation of translation / RNA binding / metal ion binding / cytosol Similarity search - Function | ||||||
Biological species | Arabidopsis thaliana (thale cress) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.186 Å | ||||||
Authors | Frank, F. / Hauver, J. / Sonenberg, N. / Nagar, B. | ||||||
Citation | Journal: Embo J. / Year: 2012 Title: Arabidopsis Argonaute MID domains use their nucleotide specificity loop to sort small RNAs. Authors: Frank, F. / Hauver, J. / Sonenberg, N. / Nagar, B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4g0o.cif.gz | 67.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4g0o.ent.gz | 50.2 KB | Display | PDB format |
PDBx/mmJSON format | 4g0o.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4g0o_validation.pdf.gz | 429.8 KB | Display | wwPDB validaton report |
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Full document | 4g0o_full_validation.pdf.gz | 433.7 KB | Display | |
Data in XML | 4g0o_validation.xml.gz | 14 KB | Display | |
Data in CIF | 4g0o_validation.cif.gz | 19.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/g0/4g0o ftp://data.pdbj.org/pub/pdb/validation_reports/g0/4g0o | HTTPS FTP |
-Related structure data
Related structure data | 4g0mC 4g0pC 4g0qC 4g0xC 4g0yC 4g0zC C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 15478.266 Da / Num. of mol.: 2 / Fragment: MID domain, UNP residues 562-699 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Arabidopsis thaliana (thale cress) / Gene: AGO5, At2g27880, T1E2.20 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 / References: UniProt: Q9SJK3 #2: Chemical | ChemComp-SO4 / | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.84 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.4 Details: 0.2M ammonium sulfate, 0.1M sodium citrate, 30% PEG4000, pH 5.4, VAPOR DIFFUSION, HANGING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5418 Å |
Detector | Type: RIGAKU SATURN 944+ / Detector: CCD / Date: Jun 8, 2010 |
Radiation | Monochromator: Varimax HF / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→30 Å / Num. all: 17087 / Num. obs: 16181 / % possible obs: 94.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 |
Reflection shell | Resolution: 2.1→2.18 Å / % possible all: 88 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.186→33.02 Å / SU ML: 0.27 / σ(F): 1.97 / Phase error: 28.52 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.86 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.31 Å2 / ksol: 0.315 e/Å3 | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: LAST / Resolution: 2.186→33.02 Å
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Refine LS restraints |
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LS refinement shell |
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